title: calibration_HindIII_70_pct_cut_30min

value: calibration sample 70%


title: calibration_HindIII_100_pct_cut_30min

status: Public on Nov 27 2019

type: SRA

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

country: Germany

institute: University Medical Center Göttingen

library_source: genomic

data_processing:
Library strategy: ORE-seq
ORE-seq: cut and uncut fragment count and resection length  After demultiplexing (Girardot et al. 2016), sequenced reads were trimmed based on basecalling quality and mapped (Li and Durbin 2009) using the combined S. cerevisiae and S. pombe reference genome. Fragments longer than 500 bp or on rDNA loci were removed. At each cut site, fragment starts and ends were counted within a sample-specific window (green areas in Fig. S1D, see Supplemental Methods) to account for exonuclease resection and within the same window the mean resection length was calculated. Uncut fragments, i.e. fragments covering, but not starting or ending at the cut site, were also counted at each cut site. Cut sites with neighbours closer than 200 bp were ignored completely and remaining cut sites with neighbours closer than 300 bp were analysed only using the starting/ending counts not pointing towards the close neighbour.  ORE-seq: occupancy estimation (cut-uncut method) See Methods and Supplemental Methods.
Calculation of ORE-seq and ODM-seq maps  For RE samples, very rare occupancy estimates outside of the interval between 0 and 1 were truncated to 0 or 1. For the ORE-seq map (Fig. 1B) we averaged the occupancy values at the same sites in different RE samples with equal weights. Similarly, for the ODM-seq map (Fig. 1B), different bisulfite samples were averaged with equal weights. We also calculated individual enzyme maps in the same way (attached as supplementary file).
BedGraph files contain the (corrected) absolute occupancy values and were generated using the R (R_Core_Team 2018) package rtracklayer (Lawrence et al. 2013).
tsv files contain columns with the absolute occupancy (corrected and not corrected), the number of effective cuts and the effective coverage for each RE site.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph, tsv

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: genomic DNA

growth_protocol: The BY4741 strain (MATa his3D0 leu2D0 met15D0 ura3D0, Euroscarf) was grown to log phase (Supplemental Fig. S1A) in YPDA medium (1% w/v Bacto yeast extract, 2% w/v Bacto peptone, 2% w/v glucose, 0.1 g/l adenine, 1 g/l KH2PO4).

extract_protocol:
Nuclei from ca. 0.1 g wet cell pellet were pre-washed in methylation buffer, centrifuged and resuspended either in 400 µl 1x CutSmart buffer (NEB) for BamHI-HF and AluI or in 1x NEB2.1 for HindIII. Digestions were started by RE addition, incubated for 30 or 120 minutes at 37°C and stopped by 10 mM EDTA and 0.5% SDS (final conc.). DNA preparation was as above. For the cut-all cut method, Schizosaccharomyces pombe gDNA, fully digested with the corresponding RE, was spiked in at 5-10% DNA mass of the final sample before phenol-chloroform extraction. After RNase A digestion, half of the sample was digested for a second time with 100 U of the corresponding RE and in the corresponding buffer for 1.5 h at 37°C. The reaction was stopped by 15 mM EDTA (final conc.).
Purified DNA was sheared to ~150 bp fragments with the Covaris S220 and concentrated using the NucleoSpin Gel and PCR Clean-up Kit (Macherey&Nagel). 0.5 – 1 µg as determined by Qubit (ThermoFisher Scientific) was used for library preparation. First, DNA was end polished (15 U T4 DNA Polymerase, 50 U T4 PNK, 5 U Klenow (NEB)) for 30 minutes at 20°C, purified with AmPure XP beads (Beckman Coulter), then subjected to A-tailing (15 U Klenow exo-(NEB)) for 30 minutes at 37°C and purified again. For adapter ligation 15 U T4 DNA Ligase (NEB) and 75 to 150 pmol NEBNext Adaptor or NEBNext Methylated Adaptor for bisulfite conversion were added. The reaction was incubated for 20 minutes at 25°C followed again by AmPure XP bead purification. Half of the end-polished and adapter ligated sample was subjected to 8 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion Polymerase (NEB). Methylated samples were bisulfite converted following the manufacturer’s instructions of the Qiagen EpiTect Bisulfite Kit. 3 µl of the converted sample was subjected to 12-14 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion U Polymerase (ThermoFisher Scientific). All samples were sequenced by LaFuGa (Illumina HiSeq 1500, 50 bp paired-end mode).

treatment_protocol: Yeast nuclei were prepared as described (Almer et al. 1986). In brief, cells were harvested by centrifugation, washed in water, resuspended in 2.8 mM EDTA, pH 8, 0.7 M 2-mercaptoethanol, incubated for 30 minutes at 30°C, washed in 1 M sorbitol, resuspended in 1 M sorbitol, 5 mM 2-mercaptoethanol and spheroplasted by incubation with 20 mg/ml freshly added Zymolyase 100T (MP Biochemicals) for 30 minutes at 30°C. Spheroplasts were washed with 1 M sorbitol and resuspended in lysis buffer (18% Ficoll, 20 mM KH2PO4, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA) followed by centrifugation at 22,550 g for 30 min to collect chromatin (“nuclei”). Pellets were frozen in dry-ice/ethanol and stored at -80°C.

tag: restriction enzyme (re)

value: HindIII

tag: strain

value: calibration sample 100%

tag: units of re/incubation time


title: calibration_HindIII_10_pct_cut_30min

value: calibration sample 10%


title: Input 19

city: Huntsville

first: Eric

middle: M

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

country: USA

institute: HudsonAlpha Institute

description:
Re-analysis of:
GSM2534237
Raw file(s):
ENCFF151WGC ENCFF147CMT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR633UAP https://www.encodeproject.org/experiments/ENCSR313ISY
Input for ATF4

data_processing:
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates and 2 controls
ChIP-seq fastqs and ChIP-seq controls were aligned to hg19 genome assembly using BWA-0.7.12(Burrows Wheeler Aligner)
Post-alignment filtering was performed using samtools with MAPQ_THRESH=30 & picard-tools-1.88 to remove the duplicates
Peak enrichment was computed using phantompeakqualtools, implementing SPP peak calling algorithm, to generate narrowpeaks
IDR was run on replicates peak file and pooled peaks, using idr-2.0.2 tool, to generate peaks passing IDR cutoff 0.02 (soft-idr-threshold) followed by filtering of ENCODE blacklisted regions
Genome_build: hg19 male
Supplementary_files_format_and_content: NarrowPeak files are in BED6+4 format with 10 tab-delimited columns [chrom ,chromStart ,chromEnd ,name ,score ,strand ,signalValue ,pValue(-log10) ,qValue(-log10) , peak]; -1 used if no pValue, qValue assigned.

organism: Homo sapiens

source_name: HepG2 cells

growth_protocol: HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)

extract_protocol:
Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol.
Illumina Single End for ChIP-seq

tag: cell line

tag: chip antibody


title: calibration_BamHI-HF_90_pct_cut_30min

value: BamHI-HF

value: calibration sample 90%


title: Input 18

description:
Re-analysis of:
GSM2534120 GSM2534356
Raw file(s):
ENCFF737ELZ ENCFF876NBT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR524VNV https://www.encodeproject.org/experiments/ENCSR716SYG
Input for ETV4
Input for HNF1A


title: Input 17

description:
Re-analysis of:
GSM2534120 GSM2533973
Raw file(s):
ENCFF434XRU ENCFF737ELZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR524VNV https://www.encodeproject.org/experiments/ENCSR381PHD
Input for FOXO1


title: calibration_BamHI-HF_70_pct_cut_30min


title: HEK293FT_miR-375_transfection_rep2_batch3

city: Cambridge

first: Sean

middle: E.

last: McGeary

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome (reference assembly hg19) using STAR v2.2 with parameters –outFilterMultimapNmax 1 –outFilterMismatchNoverLmax 0.04 –outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads Unique), and those that mapped uniquely and to ORFs were counted using htseq-count
Downstream analyses focused on the genes for which a single 3′ UTR isoform accounted for >90% of the transcripts in HeLa cells (Agarwal et al., eLife, 2014)) and those with ≥10 reads in each of the libraries.
The transfections were in 3 batches, and logTPM values were batch-normalized by fitting a linear model for each mRNA to the batch identity and transfected miRNA identity.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited text files, containing either 1.) measured logTPM values or 2.) batch-corected logTPM values for all considered mRNAs in each of the 24 miRNA transfection experiments, and a GTF file containing the transcript annotations used.

molecule: total RNA

growth_protocol: For each sample, 2.1 million HEK293FT cells  were plated in a 10 cm dish supplied with 10 mL of media (DMEM + 10% FBS) and grown for 24 hours.

extract_protocol:
RNA was extracted using TRI Reagent (Sigma-Aldrich, T9424) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing from 10 µg of total RNA per sample using standard Bioo Scientific protocols.

treatment_protocol: Cells were supplied with fresh media and transfected with 1 nmol of RNA duplex using Lipofectamine RNAiMAX (Thermo Fisher, 13778150) and Opti-MEM (Thermo Fisher, 31985062) as per the manufacturer’s protocol modified to achieve a final duplex concentration of 100 nM.

tag: miRNA

tag: rep

tag: batch


title: calibration_BamHI-HF_50_pct_cut_30min

value: calibration sample 50%


title: Input 16

description:
Re-analysis of:
GSM2534120 GSM2527623
Raw file(s):
ENCFF272WBE ENCFF737ELZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR524VNV https://www.encodeproject.org/experiments/ENCSR237LVA
Input for CREM


title: calibration_BamHI-HF_100_pct_cut_30min


title: calibration_AluI_90_pct_cut_30min

value: AluI


title: calibration_BamHI-HF_10_pct_cut_30min


title: Input 15

description:
Re-analysis of:
GSM2534120
Raw file(s):
ENCFF737ELZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR524VNV
Input for USF2


title: HEK293FT_miR-190a_transfection_rep2_batch3


title: Input 14

description:
Re-analysis of:
GSM2534060 GSM2534356
Raw file(s):
ENCFF654JMO ENCFF876NBT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR716SYG https://www.encodeproject.org/experiments/ENCSR476TKW
Input for GATA4


title: HEK293FT_miR-184_transfection_rep2_batch3


title: HEK293FT_miR-145_transfection_rep2_batch3


title: Mice_KO-2: Liver from Gpr146 KO mouse No.2

type: RNA

city: Boston

first: Haojie

last: Yu

address: 3 Blackfan Cir

department: Cardiology

institute: BIDMC

description: Gene expression data from liver of Gpr146 KO mouse

hyb_protocol: Following fragmentation, 3.5 ug of ss-cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 2.1 ST Array Strip. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station.

data_processing: The data were analyzed with using Affymetrix default analysis settings.

label: biotin

organism: Mus musculus

source_name: liver from Gpr146 KO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual target preparation for GeneChip whole transcript expression assays, 2015, Affymetrix).

growth_protocol: Male mice of 24 week-old upon chow feeding were fasted for 16 hours followed by a 6-hour refeeding

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: liver

tag: genotype

value: Gpr146 KO


title: calibration_AluI_10_pct_cut_30min


title: calibration_AluI_30_pct_cut_30min

value: calibration sample 30%


title: Mice_WT-1: Liver from Gpr146 WT mouse No.1

description: Gene expression data from liver of Gpr146 WT mouse

source_name: liver from Gpr146 WT mouse

value: Gpr146 WT


title: Mice_KO-3: Liver from Gpr146 KO mouse No.3


title: Mice_WT-2: Liver from Gpr146 WT mouse No.2


title: Input 13

description:
Re-analysis of:
GSM2533947
Raw file(s):
ENCFF434SPH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR346XJA
Input for ARID4B
Input for DNMT3B
Input for ERF
Input for FOXP1
Input for GATAD1
Input for HBP1
Input for HHEX
Input for HLF
Input for HOMEZ
Input for KLF11
Input for KMT2B
Input for MBD1_v1
Input for MBD1_v2
Input for NR2F6
Input for PBX2
Input for RERE
Input for SAP130
Input for SLC30A9
Input for SSRP1
Input for TCF25
Input for TGIF2
Input for ZNF219
Input for ZNF644
Input for ZNF792


title: Mice_WT-3: Liver from Gpr146 WT mouse No.3


title: calibration_AluI_50_pct_cut_30min


title: Mice_KO-1: Liver from Gpr146 KO mouse No.1


title: HEK293FT_miR-138_transfection_rep2_batch3


title: calibration_BamHI-HF_30_pct_cut_30min


title: in_vitro_chromatin_low_dens_GpC_80U_30min_MgCl2

data_processing:
Library strategy: ODM-seq
ODM-seq analysis for BS-seq and EM-seq data  We mapped the paired-end reads with BS-Seeker2 (version 2.1.8, (Guo et al. 2013)) using Bowtie (Langmead et al. 2009) and trimmed the reads at the real fragment ends by 5 bp to 10 bp to obtain a constant conversion ratio along reads averaged over all reads, as the conversion ratio usually shows an increase or decrease at these ends due to end repair. We ignored reads on the loci of rDNA genes and reads with an unconverted HCH motif, as HCH should be fully converted. The “anti pattern” of the CpG/GpC DNA methyltransferases is the GCH/HCG pattern, respectively, and should also be fully converted. We discarded a sample, if the average anti pattern conversion ratio among all reads was less than 0.98. At each CpG/GpC methylation site the occupancy is calculated as ratio of the converted reads over the number of all reads. We ignored methylation sites with a coverage less than 20.
Calculation of ORE-seq and ODM-seq maps  For RE samples, very rare occupancy estimates outside of the interval between 0 and 1 were truncated to 0 or 1. For the ORE-seq map (Fig. 1B) we averaged the occupancy values at the same sites in different RE samples with equal weights. Similarly, for the ODM-seq map (Fig. 1B), different bisulfite samples were averaged with equal weights (maps attached as supplementary file). We also calculated individual enzyme maps in the same way.
BedGraph files contain the absolute occupancy values and were generated using the R (R_Core_Team 2018) package rtracklayer (Lawrence et al. 2013).
tsv files contain columns with the absolute occupancy value, the strand, the motif and the number of converted as well as the total number of reads for each methyation site.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph, tsv

molecule: other

source_name: in vitro reconstituted chromatin

growth_protocol: The BY4741 strain (MATa his3D0 leu2D0 met15D0 ura3D0, Euroscarf) was grown to log phase (Supplemental Fig. S1A) in YPDA medium (1% w/v Bacto yeast extract, 2% w/v Bacto peptone, 2% w/v glucose, 0.1 g/l adenine, 1 g/l KH2PO4). Crosslinking was with 1% formaldehyde (final conc.) for 1, 5 or 20 minutes at RT while shaking and quenched for 20 min with 125 (WT1, WT4) or 250 (WT5) mM glycine (final conc.).

extract_protocol:
Nuclei pellets were washed in methylation buffer (20 mM HEPES-NaOH pH 7.5, 70 mM NaCl, 0.25 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.5% (v/v) glycerol, 1 mM DTT, 0.25 mM PMSF (Darst et al. 2012)). Per reaction, nuclei from ca. 0.1 g wet cell pellet were resuspended in 800 µl methylation buffer containing 640 µM freshly added S-adenosylmethionine (SAM). 200 U M.SssI or M.CviPI (both NEB) and 10 mM DTT were freshly added. Methylation reactions were dialyzed in Slide-A-Lyzer MINI Dialysis Devices 10 K MWCO (Thermo Fisher Scientific) against 15 ml methylation buffer with 200 µM freshly added SAM at 25°C for M.SssI or 37°C for M.CviPI. 0.5 - 1 µg fully assembled pUC19-601-25mer plasmid (pFMP233) (Lowary and Widom 1998; Lieleg et al. 2015a) and SGD assembled Escherichia coli gDNA or SGD assembled E. coli plasmid library (limited Sau3A fragments of E. coli gDNA ligated into pJET 1.2 plasmid (Thermo Fisher Scientific)) was spiked-in prior to methylase addition. E. coli spike-in results were not further pursued due to low coverage. Reactions were stopped by 0.5% SDS (final conc.), reversed crosslinked if required and DNA was deproteinized by Proteinase K, phenol-chloroform extracted and RNase A digested.
Purified DNA was sheared to ~150 bp fragments with the Covaris S220 and concentrated using the NucleoSpin Gel and PCR Clean-up Kit (Macherey&Nagel). 0.5 – 1 µg as determined by Qubit (ThermoFisher Scientific) was used for library preparation. First, DNA was end polished (15 U T4 DNA Polymerase, 50 U T4 PNK, 5 U Klenow (NEB)) for 30 minutes at 20°C, purified with AmPure XP beads (Beckman Coulter), then subjected to A-tailing (15 U Klenow exo-(NEB)) for 30 minutes at 37°C and purified again. For adapter ligation 15 U T4 DNA Ligase (NEB) and 75 to 150 pmol NEBNext Adaptor or NEBNext Methylated Adaptor for bisulfite conversion were added. The reaction was incubated for 20 minutes at 25°C followed again by AmPure XP bead purification. Half of the end-polished and adapter ligated sample was subjected to 8 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion Polymerase (NEB). Methylated samples were bisulfite converted following the manufacturer’s instructions of the Qiagen EpiTect Bisulfite Kit. 3 µl of the converted sample was subjected to 12-14 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion U Polymerase (ThermoFisher Scientific). All samples were sequenced by LaFuGa (Illumina HiSeq 1500, 50 bp paired-end mode).

tag: methyltransferase

value: GpC

value: salt gradient dialysis chromatin low density

tag: units of dnmt/incubation time

tag: chromatin stabilization

value: 1.5 mM MgCl2

tag: conversion method

value: BS-seq


title: calibration_AluI_70_pct_cut_30min


title: HEK293FT_miR-200b_transfection_rep2_batch3


title: in_vitro_chromatin_low_dens_CpG_80U_30min_MgCl2

value: CpG


title: Input 12

description:
Re-analysis of:
GSM2533944
Raw file(s):
ENCFF662ZML
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR345EZN
Input for CREB1


title: calibration_AluI_100_pct_cut_30min


title: HEK293FT_miR-133_transfection_rep2_batch3


title: in_vitro_chromatin_low_dens_CpG_80U_120min_refill_at_60min_MgCl2

value: 80 + refill/ 120 min


title: in_vitro_chromatin_low_dens_GpC_80U_120min_refill_at_60min_MgCl2


title: Input 11

description:
Re-analysis of:
GSM2527691
Raw file(s):
ENCFF929JZL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR290UXF
Input for GABPA


title: HEK293FT_miR-122_transfection_rep2_batch3


title: in_vitro_chromatin_low_dens_GpC_20U_30min_MgCl2


title: Input 10

description:
Re-analysis of:
GSM2527626 GSM2534538
Raw file(s):
ENCFF002BGD ENCFF820XYY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR855LCA https://www.encodeproject.org/experiments/ENCSR240FKS
Input for SOX13
Input for TCF7


title: in_vitro_chromatin_high_dens_GpC_80U_30min_MgCl2

value: salt gradient dialysis chromatin high density


title: Input 9

description:
Re-analysis of:
GSM2527626 GSM2534344
Raw file(s):
ENCFF002BFX ENCFF820XYY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR711HPO https://www.encodeproject.org/experiments/ENCSR240FKS
Input for ZNF189


title: HEK293FT_miR-451a_transfection_rep2_batch2


title: in_vitro_chromatin_high_dens_CpG_80U_30min_MgCl2


title: HEK293FT_miR-375_transfection_rep1_batch2


title: in_vitro_chromatin_low_dens_CpG_20U_30min_MgCl2


title: Input 8

description:
Re-analysis of:
GSM2527625
Raw file(s):
ENCFF302HDW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR239QGH
Input for KAT7
Input for KAT8
Input for KDM2A
Input for KDM3A
Input for KLF16
Input for KLF6_v2
Input for KLF9
Input for MIER2
Input for MIER3
Input for MIXL1
Input for MLX
Input for MTA1
Input for MXD3_v1
Input for MXD4
Input for NCoA2
Input for NFIA_v1
Input for NFIL3
Input for NFYC
Input for NPAS2_iso2
Input for NR2F1
Input for PAF1_v1
Input for PAXIP1_iso1
Input for PPARG_v1
Input for PRDM10
Input for RARA
Input for RCOR2
Input for RFX3_iso1
Input for RFXANK
Input for RREB1_iso2
Input for RXRB
Input for SIX4_iso1
Input for SMAD4_iso1
Input for SOX13_iso1
Input for SOX5
Input for SP1
Input for SP5
Input for TEAD1
Input for TEAD3
Input for TFDP1
Input for TFE3
Input for THAP11
Input for THRA_iso1
Input for THRB
Input for UBP1
Input for ZBTB21
Input for ZBTB26
Input for ZC3H4
Input for ZCCHC11
Input for ZFP1_v1
Input for ZFP64
Input for ZGPAT
Input for ZHX3_iso1
Input for ZKSCAN8
Input for ZNF12
Input for ZNF281
Input for ZNF331
Input for ZNF334_iso1
Input for ZNF335
Input for ZNF48
Input for ZNF511
Input for ZNF544_iso1
Input for ZNF580
Input for ZNF652
Input for ZNF7_iso2
Input for ZSCAN29_iso1
Input for ZSCAN9
Input for ARID5B
Input for BCL6_iso1
Input for CBX5
Input for CEBPA
Input for CEBPG
Input for CIZ1
Input for DMAP1
Input for DRAP1
Input for E2F7_iso1
Input for ELF3
Input for FOXA3
Input for FOXK1
Input for GABPB1_v2
Input for GATAD2A
Input for GMEB2
Input for HMG20A
Input for HMG20B_v2
Input for HMGXB3
Input for HMGXB4


title: in_vitro_chromatin_high_dens_GpC_80U_120min_refill_at_60min_MgCl2


title: Input 7

description:
Re-analysis of:
GSM2527625
Raw file(s):
ENCFF302HDW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR239QGH
Input for JARID2_iso1


title: in_vitro_chromatin_high_dens_CpG_20U_30min_MgCl2


title: in_vitro_chromatin_high_dens_CpG_80U_120min_refill_at_60min_MgCl2


title: Input 6

description:
Re-analysis of:
GSM2527623 GSM2533973
Raw file(s):
ENCFF272WBE ENCFF434XRU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR237LVA https://www.encodeproject.org/experiments/ENCSR381PHD
Input for NRF1


title: HEK293FT_miR-217_transfection_rep2_batch2


title: WT4_GpC_200U_90min

source_name: chromatin

value: BY4741- Replicate 4


title: HEK293FT_miR-219a_transfection_rep2_batch2


title: in_vitro_chromatin_high_dens_GpC_20U_30min_MgCl2


title: H18_input_ChIP_R2

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Reads were mapped using STAR (v.2.4.2a) for RNA-seq to galGal5. Read counts were obtained using subread (v.1.4.5) FeatureCounts. For ChIP-seq, reads were mapped using bowtie to gg5 genome
Differential Expression analysis was performed using DESeq2 R package. Diffbind package was used for ChIP-seq experiment
Genome_build: galGal5

organism: Gallus gallus

growth_protocol: Fertilised wild-type chicken eggs were obtained from Henry Stewart & Co (Norfolk), staged according to Hamburger and Hamilton (1951) (24). All experiments were performed on chicken embryos younger than 12 days of development, and as such were not regulated by the Animals (Scientific Procedures) Act 1986.

extract_protocol:
FAC-sorted cells were washed with PBS and stored at 80°C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (Cat.#AM1931, ThermoFisher Scientific), the integrity was checked using Bioanalyser, and only samples with RIN>6 were used for analysis.  Bioin ChIP-seq was carried out using previously described protocol following crosslinking, sonication and library preparation
RNA-seq libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Cat.#634889, Takara Bio Clontech) and sequenced using 40bp paired-end reads on Illumina NextSeq500. Biotin ChIP-seq libraries were prepared using MicroPlex library preparation kit v2 (Diagnode) and sequenced using 40 bp paired-end reads on Illumina NextSeq500 with a 75 cycle kit.

treatment_protocol: Dissected vagal regions from electroporated embryos were dissociated with dispase (1.5mg/ml in DMEM/10mM Hepes pH 7.5) at 37°C for 15min with intermittent pipetting to achieve a single cell suspension and 0.05% Trypsin at 37°C for a final 3min. The reaction was stopped and cells were resuspended in an excess of Hanks buffer. Cells were centrifuged at 500g for 10min and resuspended in Hanks buffer, passed through a 0.22mm filter and centrifuged at 750g for 10min, pelleted cells were resuspended in 500µl Hanks buffer. Fluorescent positive cells were sorted and collected using BD FACS-Aria Fusion.

tag: genotype/variation

value: Wild-type

tag: development

value: Embryo

value: Neural crest (E2+ cells)

value: Dissociation and FACS

tag: treatment

value: E2:citrine electroporation at HH8

tag: amplification

tag: assay

value: Biotin ChIP-seq


title: Input 5

description:
Re-analysis of:
GSM2527616
Raw file(s):
ENCFF105CNG
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR226ULX
Input for RAD21


title: WT4_CpG_200U_90min

tag: strain


title: WT4_GpC_200U_45min


title: Input 1

description:
Raw file(s):
ENCFF035QZC ENCFF160YIT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR856HWY https://www.encodeproject.org/experiments/ENCSR384OZQ
Input for ZNF3

tag: cell line


title: HEK293FT_miR-216a_transfection_rep2_batch2


title: HEK293FT_miR-190a_transfection_rep1_batch2


title: HEK293FT_miR-200b_transfection_rep1_batch2


title: ZSCAN9

description:
Re-analysis of:
GSM2534346 GSM2534345
Raw file(s):
ENCFF257FGF ENCFF772XOL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR712FAM

tag: chip antibody


title: ZNF7_iso2

description:
Re-analysis of:
GSM2534140 GSM2534141
Raw file(s):
ENCFF079AGT ENCFF753ADO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR553QMC


title: WT4_CpG_200U_15min


title: HEK293FT_miR-451a_transfection_rep1_batch1

tag: miRNA


title: WT4_GpC_200U_15min


title: HEK293FT_miR-138_transfection_rep1_batch2

tag: rep


title: ZNF792

description:
Re-analysis of:
GSM2533985 GSM2533984
Raw file(s):
ENCFF503DWZ ENCFF414QOO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR396SOH


title: H18_sox10_ChIP_R2

value: MicroPlex library preparation kit v2 (Diagnode)


title: ZNF652

description:
Re-analysis of:
GSM2534081 GSM2534082
Raw file(s):
ENCFF372LTI ENCFF061MRR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR502GAX


title: H18_sox10_ChIP_R1


title: WT4_GpC_200U_240min_refill_at_180min

value: 200 + refill/ 240 min


title: H10_RNA

value: Neural crest (NC2+ cells)

value: NC2:citrine electroporation at HH4

value: Illumina Nextera XT library preparation kit

value: RNA-seq


title: HEK293FT_miR-219a_transfection_rep1_batch1

tag: batch


title: WT4_CpG_200U_240min_refill_at_180min

value: BS-seq


title: HEK293FT_miR-216a_transfection_rep1_batch1


title: WT4_CpG_200U_45min

value: CpG


title: WT3_GpC_200U_90min

value: GpC

value: BY4741- Replicate 3


title: cas9_control_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt

data_processing:
Reads were mapped using STAR (v.2.4.2a) for RNA-seq to galGal5. Read counts were obtained using subread (v.1.4.5) FeatureCounts
Differential Expression analysis was performed using DESeq2 R package.
Genome_build: galGal5

extract_protocol:
RNA was extracted from dissected half dorsal neural tubes using Ambion RNAqueous Micro Total RNA isolation kit (Cat.#AM1931, ThermoFisher Scientific), the integrity was checked using Bioanalyser, and only samples with RIN>6 were used for analysis.
RNA-seq libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Cat.#634889, Takara Bio Clontech) and sequenced using 40bp paired-end reads on Illumina NextSeq500.

tag: tissue

value: Neural crest (Cit+ cells)

value: pCAG Cas9-2A-Citrine


title: ZNF644

description:
Re-analysis of:
GSM2534180 GSM2534181
Raw file(s):
ENCFF095XXT ENCFF272TAW
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR578CXC


title: WT3_CpG_200U_90min


title: ZNF580

description:
Re-analysis of:
GSM2527559 GSM2527558
Raw file(s):
ENCFF099NTW ENCFF720DMM
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR173CTF


title: ZNF511

description:
Re-analysis of:
GSM2533962 GSM2533961
Raw file(s):
ENCFF259MWS ENCFF128OQA
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR372JXR


title: HEK293FT_miR-145_transfection_rep1_batch1


title: ZNF48

description:
Re-analysis of:
GSM2534005 GSM2534006
Raw file(s):
ENCFF287ADI ENCFF521IXY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR415AEB


title: dko_KO_RNA_R3

description:
Wild-type
RNA_featurecounts_KO.txt

value: Wild-type

value: Embryo

value: pcU6:tfap2b_g1, pcU6:tfap2b_g2, pU6:sox10_g1, pCAG Cas9-2A-Citrine


title: HEK293FT_miR-184_transfection_rep1_batch1


title: WT3_GpC_200U_45min


title: cas9_control_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt

value: Dissociation and FACS


title: WT3_CpG_200U_45min


title: HEK293FT_miR-133_transfection_rep1_batch1


title: dko_KO_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt


title: ZNF3

description:
Raw file(s):
ENCFF296DPR ENCFF656IHM
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR182QWU


title: HEK293FT_miR-217_transfection_rep1_batch1


title: ZNF189

description:
Raw file(s):
ENCFF991BHB_in_progress ENCFF710RSW_in_progress
can be retrieved from ENCODE:
ENCFF710RSW_in_progress ENCFF991BHB


title: dko_KO_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt


title: tfap2b_KO_RNA_R3

description:
Wild-type
RNA_featurecounts_KO.txt

value: pcU6:tfap2b_g1, pcU6:tfap2b_g2, pCAG Cas9-2A-Citrine


title: ZMYM3


title: WT3_CpG_200U_45min_MgCl2

value: 3 mM MgCl2


title: HeLa_miR-223_transfection_rep2_batch5

data_processing:
Reads were aligned to the human genome (reference assembly hg19) using STAR v2.2 with parameters –outFilterMultimapNmax 1 –outFilterMismatchNoverLmax 0.04 –outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads Unique), and those that mapped uniquely and to ORFs were counted using htseq-count
Downstream analyses focused on the genes for which a single 3′ UTR isoform accounted for >90% of the transcripts in HeLa cells (Agarwal et al., eLife, 2014)) and those with ≥10 reads in each of the libraries.
The transfections were in 5 batches, and logTPM values were batch-normalized by fitting a linear model for each mRNA to the batch identity and transfected miRNA identity.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited text files, containing either 1.) measured logTPM values or 2.) batch-corected logTPM values for all considered mRNAs in each of the 34 miRNA transfection experiments, and a GTF file containing thetranscript annotations used.

source_name: HeLa

growth_protocol: For each sample, 2.5 million HeLa cells  were plated in a 10 cm dish supplied with 10 mL of media (DMEM + 10% FBS) and grown for 24 hours.

value: HeLa


title: HeLa_miR-216b_transfection_rep2_batch5


title: tfap2b_KO_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt


title: ZKSCAN8

description:
Re-analysis of:
GSM2534470 GSM2534469
Raw file(s):
ENCFF824RXN ENCFF006ALN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR808FFI


title: HeLa_miR-153_transfection_rep2_batch5


title: HeLa_miR-143_transfection_rep2_batch5


title: WT3_GpC_200U_15min


title: WT3_CpG_200U_180min


title: sox10_KO_RNA_R3

description:
Wild-type
RNA_featurecounts_KO.txt

value: pcU6:sox10_g1, pcU6:sox10_g2, pCAG Cas9-2A-Citrine


title: tfap2b_KO_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt


title: HeLa_miR-124_transfection_rep2_batch5


title: ZFP64

description:
Re-analysis of:
GSM2534066 GSM2534065
Raw file(s):
ENCFF493APP ENCFF213TBR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR487CPI


title: WT3_GpC_200U_240min_refill_at_180min

value: 200 + refill/ 240 min


title: WT3_CpG_200U_15min


title: HeLa_miR-1_transfection_rep2_batch5


title: sox10_KO_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt

value: Illumina Nextera XT library preparation kit


title: WT3_GpC_200U_45min_MgCl2


title: ZGPAT

description:
Re-analysis of:
GSM2534339 GSM2534338
Raw file(s):
ENCFF885OGQ ENCFF379UBY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR704IGU

value: FLAG-ZGPAT


title: ZFP1_v1

description:
Re-analysis of:
GSM2534186 GSM2534187
Raw file(s):
ENCFF868BZO ENCFF962UNX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR586DEH


title: HEK293FT_miR-122_transfection_rep1_batch1


title: sox10_KO_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt

value: RNA-seq


title: WT3_CpG_200U_240min_refill_at_180min

value: CpG

value: BS-seq


title: HeLa_lsy-6_transfection_rep2_batch5


title: WT3_GpC_200U_180min

value: GpC

value: BY4741- Replicate 3


title: WT3_GpC_200U_150min_refill_at_90min_MgCl2

value: 200 + refill/ 150 min


title: ZHX2

description:
Re-analysis of:
GSM2534001 GSM2534002
Raw file(s):
ENCFF002BFE ENCFF002BFF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR407BEZ


title: USF2


title: HeLa_let-7a_transfection_rep2_batch5


title: HeLa_miR-182_transfection_rep2_batch4


title: WT3_CpG_200U_150min_refill_at_90min_MgCl2


title: msx1_KO_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt

value: Wild-type

value: Neural crest (Cit+ cells)

value: pcU6:msx1, pCAG Cas9-2A-Citrine


title: msx1_KO_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt

value: Embryo

value: Dissociation and FACS


title: THRB

description:
Re-analysis of:
GSM2534017 GSM2534018
Raw file(s):
ENCFF805RHK ENCFF675YZO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR430JGJ

value: FLAG-THRB


title: HeLa_miR-155_transfection_rep2_batch4

value: HeLa


title: sox3_KO_RNA_R2

description:
Wild-type
RNA_featurecounts_KO.txt

value: pcU6:sox3_g1, pcU6:sox3_g2, pCAG Cas9-2A-Citrine


title: THAP11

description:
Re-analysis of:
GSM2534159 GSM2534158
Raw file(s):
ENCFF371NAN ENCFF345EHR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR562POI


title: HeLa_miR-139_transfection_rep2_batch4


title: sox3_KO_RNA_R1

description:
Wild-type
RNA_featurecounts_KO.txt


title: TGIF2

description:
Re-analysis of:
GSM2534722 GSM2534723
Raw file(s):
ENCFF490CEX ENCFF968PBN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR993LMB


title: HeLa_miR-124_transfection_rep1_batch4


title: H25neg_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

extract_protocol:
FAC-sorted cells were washed with PBS and stored at 80°C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (Cat.#AM1931, ThermoFisher Scientific), the integrity was checked using Bioanalyser, and only samples with RIN>6 were used for analysis.
RNA-seq libraries were prepared using SMART-Seq™ v4 Ultra™ Low Input RNA Kit for Sequencing (Cat.#634889, Takara Bio Clontech) and sequenced using 40bp paired-end reads on Illumina NextSeq500.

value: Negative control (NC2-, E2- cells)

value: NC2:citrine, E2:citrine electroporation at HH8/9


title: WT3_GpC_100U_45min_MgCl2

value: 3 mM MgCl2


title: WT5_xl_5_GpC_400U_90min

value: BY4741 crosslinked 5 min - Replicate 5

value: crosslinked cells


title: TFE3

description:
Re-analysis of:
GSM2534191 GSM2534190
Raw file(s):
ENCFF851FHG ENCFF085MHP
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR589SNT


title: TFDP1

description:
Raw file(s):
ENCFF718NVN_in_progress ENCFF260ZRQ_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR558OMR


title: HeLa_miR-7_transfection_rep2_batch4


title: H25neg_RNA_R1

description:
Wild-type
RNA_featurecounts.txt

value: Illumina Nextera XT library preparation kit

value: RNA-seq


title: ZBTB26

description:
Re-analysis of:
GSM2527571 GSM2527572
Raw file(s):
ENCFF928MCL ENCFF649ROJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR184SVO


title: HeLa_miR-1_transfection_rep1_batch4


title: WT5_xl_5_CpG_200U_90min

value: CpG

value: BS-seq


title: H25E2_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

value: Wild-type

value: Neural crest (NC2-, E2+ cells)


title: msx1_KO_RNA_R3

description:
Wild-type
RNA_featurecounts_KO.txt

value: Neural crest (Cit+ cells)

value: pcU6:msx1, pCAG Cas9-2A-Citrine


title: WT5_xl_5_CpG_200U_180min_refill_at_90min

value: 200 + refill/180 min


title: TEAD3

description:
Re-analysis of:
GSM2534287 GSM2534286
Raw file(s):
ENCFF192BLY ENCFF770VIU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR666QNP


title: HeLa_lsy-6_transfection_rep1_batch4


title: WT5_xl_5_CpG_200U_180min_EM-seq_refill_at_90min

value: EM-seq


title: HeLa_let-7a_transfection_rep1_batch4

value: HeLa


title: WT3_CpG_100U_45min_MgCl2

value: BY4741- Replicate 3


title: TFAP4

description:
Re-analysis of:
GSM2527463 GSM2527464
Raw file(s):
ENCFF822SMI ENCFF813TPE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR103SZL


title: WT5_xl_20_GpC_400U_90min

value: GpC

value: BY4741 crosslinked 20 min - Replicate 5


title: TEAD1

description:
Re-analysis of:
GSM2534071 GSM2534072
Raw file(s):
ENCFF703VJZ ENCFF974TAR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR497JLX


title: TCF7

description:
Re-analysis of:
GSM2534030 GSM2534031
Raw file(s):
ENCFF204ZXN ENCFF153EWU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR444LIN


title: WT5_xl_5_GpC_400U_180min_refill_at_90min

value: 400 + refill/180 min


title: WT5_xl_20_GpC_400U_180min_refill_at_90min


title: SSRP1

description:
Re-analysis of:
GSM2534175 GSM2534174
Raw file(s):
ENCFF568WKI ENCFF925BQC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR571PDN


title: HeLa_miR-216b_transfection_rep1_batch3


title: H25DP_RNA_R1

description:
Wild-type
RNA_featurecounts.txt

value: Embryo

value: Neural crest (NC2+, E2+ cells)

value: Dissociation and FACS

value: NC2:citrine, E2:citrine electroporation at HH8/9


title: H18neg_R2

description:
Wild-type
RNA_featurecounts.txt

value: Negative control (NC2-, E2- cells)

value: Illumina Nextera XT library preparation kit

value: RNA-seq


title: HeLa_miR-182_transfection_rep1_batch3


title: H18neg_R1

description:
Wild-type
RNA_featurecounts.txt

value: Wild-type


title: SP5

description:
Re-analysis of:
GSM2527397 GSM2527396
Raw file(s):
ENCFF731JAM ENCFF249QKO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR019NPF


title: HeLa_miR-153_transfection_rep1_batch3


title: HeLa_miR-205_transfection_rep2_batch3


title: WT5_xl_20_CpG_200U_180min_refill_at_90min

value: CpG

value: crosslinked cells

value: BS-seq


title: SOX5

description:
Re-analysis of:
GSM2534683 GSM2534682
Raw file(s):
ENCFF887ZSW ENCFF674UHN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR961WLZ


title: HeLa_miR-139_transfection_rep1_batch3


title: H18E2_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

value: Neural crest (NC2-, E2+ cells)


title: H25E2_RNA_R1

description:
Wild-type
RNA_featurecounts.txt


title: H18E2_RNA_R1

description:
Wild-type
RNA_featurecounts.txt


title: SOX13_iso1

description:
Re-analysis of:
GSM2534355 GSM2534354
Raw file(s):
ENCFF336VLV ENCFF892EKB
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR715UCI


title: H18DP_RNA_R2

description:
Wild-type
RNA_featurecounts.txt


title: WT5_xl_1_GpC_400U_180min_refill_at_90min

value: BY4741 crosslinked 1 min - Replicate 5


title: WT5_xl_1_GpC_400U_90min


title: HeLa_miR-7_transfection_rep1_batch3

value: HeLa


title: HeLa_miR-137_transfection_rep2_batch3


title: WT5_xl_20_CpG_200U_180min_EM-seq_refill_at_90min

value: 200 + refill/180 min

value: EM-seq


title: H18DP_RNA_R1

description:
Wild-type
RNA_featurecounts.txt


title: WT5_xl_20_CpG_200U_90min

value: BY4741 crosslinked 20 min - Replicate 5


title: HeLa_miR-223_transfection_rep1_batch2


title: WT5_xl_1_CpG_200U_90min


title: SMAD4_iso1

description:
Re-analysis of:
GSM2534492 GSM2534491
Raw file(s):
ENCFF633XUQ ENCFF438SXQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR826YMT


title: SLC30A9

description:
Re-analysis of:
GSM2534261 GSM2534262
Raw file(s):
ENCFF088SMS ENCFF698KPI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR654ORQ


title: SAP130

description:
Re-analysis of:
GSM2534677 GSM2534678
Raw file(s):
ENCFF268REE ENCFF482RBF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR959OMS


title: H25DP_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

value: Embryo


title: HeLa_miR-205_transfection_rep1_batch2


title: WT5_xl_1_CpG_200U_180min_refill_at_90min

value: 200 + refill/ 180 min


title: H10neg_RNA_R1

description:
Wild-type
RNA_featurecounts.txt

value: Negative control (NC2- , E2- cells)

value: Dissociation and FACS

value: NC2:citrine, E2:citrine electroporation at HH4


title: WT4_xl_GpC_200U_90min

value: GpC

value: BY4741 crosslinked - Replicate 4


title: HeLa_miR-204_transfection_rep2_batch2


title: H10E2_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

value: Wild-type

value: Illumina Nextera XT library preparation kit

value: RNA-seq


title: HeLa_miR-199a_transfection_rep2_batch2


title: RXRB

description:
Re-analysis of:
GSM2534153 GSM2534152
Raw file(s):
ENCFF174QLC ENCFF256YDZ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR560SEP

value: FLAG-RXRB


title: WT4_xl_CpG_200U_90min

value: CpG

value: crosslinked cells

value: BS-seq


title: H10E2_RNA_R1

description:
Wild-type
RNA_featurecounts.txt

value: Neural crest (NC2-, E2+ cells)


title: WT4_xl_GpC_200U_45min


title: SOX13

description:
Re-analysis of:
GSM2534032 GSM2534033
Raw file(s):
ENCFF939TTG ENCFF137GGC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR445ACU


title: HeLa_miR-155_transfection_rep1_batch2

value: HeLa


title: H25neg_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

data_processing:
Reads were mapped using  Bowtie  (v.1.0.0) to galGal5.
Peak calling was performed using MACS2, de novo motif search was performed using Homer (v.4.7)
Genome_build: galGal5

extract_protocol:
FAC-sorted cells were lysed (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal) and tagmented using Illumina Nextera DNA kit (FC-121-1030) for 20mins at 37°C. Tagmented DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix for 11 cycles. Tagmentation efficiency was assessed using Agilent Tapestation. Three biological replicates were obtained for each stage.
Libraries were prepared using Illumina Nextera DNA kit and sequenced on Illumina NextSeq500 using 40bp paired end reads

value: Negative control (NC2-, E2- cells)

value: NC2:citrine, E2:citrine electroporation at HH8/9

value: ATAC-seq


title: RUVBL1


title: HeLa_miR-144_transfection_rep2_batch2


title: H25neg_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Embryo

value: NEB Next High-Fidelity 2X PCR Master Mix


title: WT4_xl_CpG_200U_45min


title: RFX3_iso1

description:
Re-analysis of:
GSM2534236 GSM2534235
Raw file(s):
ENCFF383FTW ENCFF068PBQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR633OVO


title: HeLa_miR-143_transfection_rep1_batch2


title: WT4_xl_GpC_200U_45min_MgCl2

value: 3 mM MgCl2 + crosslinked cells


title: H10neg_RNA_R2

description:
Wild-type
RNA_featurecounts.txt

value: Dissociation and FACS

value: NC2:citrine, E2:citrine electroporation at HH4


title: H25neg_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type


title: HeLa_miR-137_transfection_rep1_batch2


title: WT4_xl_CpG_200U_45min_MgCl2

value: BY4741 crosslinked - Replicate 4


title: RERE

description:
Re-analysis of:
GSM2534719 GSM2534718
Raw file(s):
ENCFF811ZQF ENCFF266MCK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR988ZSI

value: FLAG-RERE


title: HeLa_miR-204_transfection_rep1_batch1


title: RCOR2

description:
Re-analysis of:
GSM2534039 GSM2534040
Raw file(s):
ENCFF040QAY ENCFF763NHP
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR455DOO


title: WT4_xl_GpC_200U_15min

value: GpC


title: RARA

description:
Re-analysis of:
GSM2534075 GSM2534076
Raw file(s):
ENCFF308NXH ENCFF320DMI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR500WXT

value: FLAG-RARA


title: H25E2_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt


title: H25E2_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt


title: H25E2_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt


title: WT4_xl_CpG_200U_15min

value: CpG

value: crosslinked cells


title: RAD21

description:
Re-analysis of:
GSM2527412 GSM2527413
Raw file(s):
ENCFF801MAM ENCFF822AJG
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR054FKH


title: H25DP_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Neural crest (NC2+, E2+ cells)


title: WT4_xl_GpC_200U_240min_refill_at_180min

value: 200 + refill/ 240 min

value: BS-seq


title: HeLa_miR-144_transfection_rep1_batch1

value: HeLa


title: PROX1


title: mpra_miR-7_rep2

data_processing:
Each read was used if it satisfied the following criteria: 1) it passed the Illumina chastity filter, as indicated by the presence of the number 1 rather than 0 in the final position of the fastq header line, 2) it did not contain any “N” base calls, 3) it did not contain any positions with a Phred quality score (Q) of B or lower, 4) the sequenced 6-nt sample-multiplexing barcode associated with the read was identical to one of the barcodes used when generating the sequencing library, and 5) it did not match either strand of the phi-X genome.
Reads were queried against a list of the 100-nt sequences downstream of the sequencing-primer site in the reporter mRNA 3′ UTR, requiring a perfect match.
Counts were normalized to the total number of perfectly matching reads to obtain counts-per-million (cpm) values.
Genome_build: NA
Supplementary_files_format_and_content: A tab delimited text file containing the counts-per-million (cpm) corresponding to the abundance of each of the 29,992 designed reporter variants in each of the 12 samples.

growth_protocol: For each sample, 0.724 million HeLa cells were plated in a 10 cm dish supplied with 10 mL of media (DMEM + 10% FBS) and grown for 24 hours.

extract_protocol:
RNA was extracted according to the methods.
Small RNA-seq libraries were prepared according to the methods.

treatment_protocol: Cells were supplied with fresh media and transfected using Lipofectamine RNAiMAX (Thermo Fisher, 13778150) and Opti-MEM (Thermo Fisher, 31985062) as per the manufacturer’s protocol modified to achieve a final duplex concentration of 144 nM. After 24 h of culture, the cells were supplied with fresh media and transfected with 5.8 µg of reporter library diluted in 28.9 µg of pUC19 carrier plasmid using Lipofectamine 2000 (Thermo Fisher, 11668019) as per the manufacturer’s protocol.


title: RFXANK

description:
Re-analysis of:
GSM2534485 GSM2534484
Raw file(s):
ENCFF895HBS ENCFF958ONK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR823ADL

value: FLAG-RFXANK


title: H25DP_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Embryo

value: NC2:citrine, E2:citrine electroporation at HH8/9

value: ATAC-seq


title: PPARG_v1

description:
Re-analysis of:
GSM2527505 GSM2527506
Raw file(s):
ENCFF660VHF ENCFF764SMY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR130VQL


title: mpra_miR-7_rep1


title: WT4_xl_CpG_200U_240min_refill_at_180min


title: H25DP_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Dissociation and FACS

value: NEB Next High-Fidelity 2X PCR Master Mix


title: PBX2

description:
Re-analysis of:
GSM2534526 GSM2534527
Raw file(s):
ENCFF395VGH ENCFF967ZPY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR849DFF


title: PAF1_v1

description:
Re-analysis of:
GSM2533916 GSM2533915
Raw file(s):
ENCFF896YTL ENCFF294AGC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR327RFM


title: H18neg_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type

value: Negative control (NC2-, E2- cells)


title: mpra_lsy-6_rep2


title: mpra_lsy-6_rep1


title: H18neg_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt


title: HeLa_miR-199a_transfection_rep1_batch1


title: H18neg_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt


title: mpra_miR-124_rep2


title: NR2F6

description:
Re-analysis of:
GSM2534449 GSM2534450
Raw file(s):
ENCFF095AEN ENCFF862ZWK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR798IJO


title: NRF1

description:
Re-analysis of:
GSM2534537 GSM2534536
Raw file(s):
ENCFF045UOH ENCFF468UEL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR853ADA


title: mpra_miR-124_rep1


title: NR2F1

description:
Re-analysis of:
GSM2534285 GSM2534284
Raw file(s):
ENCFF325WEY ENCFF911VFY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR662EOU


title: WT4_xl_CpG_100U_45min_MgCl2

value: BY4741 crosslinked - Replicate 4

value: 3 mM MgCl2 + crosslinked cells


title: WT1_xl_GpC_200U_90min

value: GpC

value: BY4741 crosslinked - Replicate 1


title: WT1_xl_CpG_200U_90min

value: CpG

value: crosslinked cells


title: H18E2_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Neural crest (NC2-, E2+ cells)


title: mpra_miR-155_rep2


title: mpra_miR-155_rep1


title: H18E2_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt


title: NR1H2


title: WT1_xl_GpC_200U_45min

value: BS-seq


title: H18E2_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt


title: WT4_xl_GpC_200U_150min_refill_at_90min_MgCl2

value: 200 + refill/ 150 min


title: WT4_xl_CpG_200U_150min_refill_at_90min_MgCl2


title: NFYC

description:
Re-analysis of:
GSM2534171 GSM2534172
Raw file(s):
ENCFF117DNV ENCFF536WLP
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR569ARC

value: FLAG-NFYC


title: WT4_xl_GpC_100U_45min_MgCl2


title: H18DP_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Embryo

value: Neural crest (NC2+, E2+ cells)


title: mpra_let-7a_rep2


title: WT1_xl_CpG_200U_45min_MgCl2


title: mpra_miR-1_rep2


title: mpra_let-7a_rep1


title: WT1_xl_GpC_200U_150min_refill_at_90min_MgCl2


title: NCoA2

description:
Raw file(s):
ENCFF853OPO_in_progress ENCFF958CKR_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR631AVZ https://www.encodeproject.org/experiments/ENCSR631AVZ


title: H10E2_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Neural crest (E2+ cells)

value: NC2:citrine, E2:citrine electroporation at HH4

value: ATAC-seq


title: mpra_miR-1_rep1


title: MXD4

description:
Re-analysis of:
GSM2534026 GSM2534025
Raw file(s):
ENCFF393OKM ENCFF480HVG
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR441KFW


title: In Vitro 2 [IV2]

first: Devon

last: Svoboda

email: svobodadevon@gmail.com, barc@wi.mit.edu

address: 455 Main St

institute: Whitehead Institute

description: 657 iPSCs were reprogrammed from fibroblasts (Couriel) and targetted to express GFP constitutively.

data_processing:
Fastq files were obtained with using "cellranger mkfastq" (Cell Ranger v3 from 10x Genomics).
Demultiplexing, mapping and gene counting were performed with "cellranger count", Cell Ranger 3.0.2 from 10x Genomics.
For samples IV1 and IV2, mapping was done against the human release hg18 plus the sequence coding for the green fluorences protein EGFP. For the other 4 samples Mapping was done  against a combined genome containing hg18, mm10 amd the sequence coding for the green fluorences protein EGFP.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_gene_bc_matrices text output files from Cell Ranger count.

molecule: polyA RNA

source_name: GFP+ in vitro differentiated microglia

growth_protocol: Microglial Precursors from 657-GFP iPS cell line using protocol published in Douvaras et al. 2017.  Further differentiated in vitro using a new media containing TGFB1, CSF1 and IL34 published in Svoboda et al., 2019, PNAS.

extract_protocol:
In vivo samples were extracted by homogenizing the mouse brain on ice and FACS sorting out GFP+ cells for library construction.  In vitro samples were extracted by detaching cells from the cell culture dish using EDTA, running cells through the brain homogenization protocol to control for effects of protocol, and FACS sorting GFP+ cells. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps. Cell count was determined using Countess II.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns PN-1000075, according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

tag: source detailed

value: In Vitro Differentiated microglia

tag: cell type

value: 657-GFP iPS cell line


title: H10E2_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type

value: Dissociation and FACS

value: NEB Next High-Fidelity 2X PCR Master Mix


title: MXD3_v1

description:
Re-analysis of:
GSM2534621 GSM2534622
Raw file(s):
ENCFF380ESC ENCFF204UTF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR909GJR


title: MLX

description:
Re-analysis of:
GSM2527496 GSM2527497
Raw file(s):
ENCFF771RGQ ENCFF082XMQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR125DAD

value: FLAG-MLX


title: WT1_xl_GpC_200U_240min_refill_at_180min

tag: methyltransferase

value: GpC

value: BY4741 crosslinked - Replicate 1

tag: units of dnmt/incubation time

value: 200 + refill/ 180 min


title: In Vitro 1 [IV1]


title: In Vivo 3 [M2]

source_name: GFP+ cells from chimeric mouse brain

value: From NSG-Tg(Hu-SCF, GM-CSF, IL-3, CSF1) chimeric mouse


title: WT1_xl_CpG_200U_240min_refill_at_180min

value: CpG

value: 200 + refill/ 240 min

tag: chromatin stabilization

value: crosslinked cells

tag: conversion method

value: BS-seq


title: NFIL3

description:
Re-analysis of:
GSM2527591 GSM2527590
Raw file(s):
ENCFF170AOL ENCFF149FLF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR201GGK


title: WT1_xl_CpG_200U_45min


title: H10_neg_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

tag: development

value: Embryo

value: Negative control (NC2- cells)

value: NC2:citrine electroporation at HH4


title: In Vivo 4 [M1]


title: WT1_xl_CpG_200U_150min_refill_at_90min_MgCl2

value: 200 + refill/ 150 min

value: 3 mM MgCl2 + crosslinked cells


title: MIXL1

description:
Re-analysis of:
GSM2534689 GSM2534688
Raw file(s):
ENCFF616WVB ENCFF790RMU
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR966PJY


title: H18DP_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type

value: Neural crest (NC2+, E2+ cells)

tag: treatment

value: NC2:citrine, E2:citrine electroporation at HH8/9

value: ATAC-seq


title: MIER3

description:
Re-analysis of:
GSM2534128 GSM2534127
Raw file(s):
ENCFF823JNT ENCFF352WCY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR531VIJ


title: H10_neg_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Dissociation and FACS

tag: amplification

value: NEB Next High-Fidelity 2X PCR Master Mix


title: NFIA_v1

description:
Re-analysis of:
GSM2527614 GSM2527615
Raw file(s):
ENCFF784EQQ ENCFF908GXH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR226QQM


title: In vitro iMG 60dpi rep 6

data_processing:
Reads were mapped to the combined human (GRCh38) and mouse (GRCm38) genomes (canonical chromosomes only) with STAR (2.7.1a), using default parameters.
Human gene counts were obtained with HOMER (analyzeRepeats.pl) using Ensembl 93 gene models and options "-raw -count exons -strand both -condenseGenes".
Genome_build: GRCh38 + GRCm38
Supplementary_files_format_and_content: Ensembl gene ID, counts (tab-delimited format)

source_name: In vitro differentiated microglia 60d

extract_protocol:
Qiagen microRNeasy+ kit according to manufacturers protocol.
3 ng of RNA was used as input using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines.
RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA.  The amount of cDNA between 100-3000 bp was calculated by Fragment Analyzer and Qubit.  150pg of the sample in range was then added to Illumina’s Nextera XT and processed according to manufacturer’s guidelines.  Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and unique dual indexes were added by PCR amplification.  Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II.  All libraries were then pooled and sequenced at single-end 40 base-pair using the Illumina HiSeq 2500.

tag: cell line source

value: Derived from iPS line 657-GFP

value: In vitro differentiated microglia

tag: replicate

value: Biological replicate 6


title: H18DP_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

tag: strain

tag: assay


title: MIER2

description:
Re-analysis of:
GSM2527485 GSM2527484
Raw file(s):
ENCFF919DQH ENCFF962ZIJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR115PIK

tag: cell line

tag: chip antibody


title: WT1_xl_CpG_100U_45min_MgCl2

value: CpG

value: BY4741 crosslinked - Replicate 1


title: WT1_xl_GpC_100U_45min_MgCl2

value: GpC

value: BS-seq


title: WT1_xl_CpG_200U_180min

value: crosslinked cells


title: WT1_xl_GpC_200U_180min


title: H10_neg_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Embryo

value: Negative control (NC2- cells)

value: NC2:citrine electroporation at HH4


title: H10NC2_ATAC_R3

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type

value: Neural crest (NC2+ cells)


title: MBD1_v2

description:
Re-analysis of:
GSM2527645 GSM2527644
Raw file(s):
ENCFF617BUV ENCFF844LMK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR260UJI


title: H10NC2_ATAC_R2

description:
Wild-type
ATAC_featurecounts_raw.txt


title: In vitro iMG 60dpi rep 4

value: Biological replicate 4


title: WT1_GpC_200U_45min_MgCl2

value: BY4741 - Replicate 1

value: 3 mM MgCl2


title: H10E2_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Neural crest (E2+ cells)

value: Dissociation and FACS

value: NC2:citrine, E2:citrine electroporation at HH4

value: NEB Next High-Fidelity 2X PCR Master Mix

value: ATAC-seq


title: In vitro iMG 60dpi rep 5

value: Derived from iPS line 657-GFP

value: In vitro differentiated microglia

value: Biological replicate 5


title: WT1_CpG_200U_45min_MgCl2

value: CpG

value: BS-seq


title: KMT2B

description:
Re-analysis of:
GSM2527431 GSM2527432
Raw file(s):
ENCFF714SGI ENCFF247HTV
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR071YVR


title: MBD1_v1

description:
Re-analysis of:
GSM2533983 GSM2533982
Raw file(s):
ENCFF707YEY ENCFF690UNT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR396QWK


title: In vitro iMG 60dpi rep 3

value: Biological replicate 3


title: WT1_GpC_200U_150min_refill_at_90min_MgCl2

value: GpC

value: 200 + refill/ 150 min


title: H10NC2_ATAC_R1

description:
Wild-type
ATAC_featurecounts_raw.txt

value: Wild-type

value: Embryo

value: Neural crest (NC2+ cells)

value: NC2:citrine electroporation at HH4


title: In vitro iMG 60dpi rep 2

value: Biological replicate 2


title: Wagner_Dmel_DL1_IntS11+E203Qrescue_RNA-seq

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
ATAC-seq read pairs containing one or more members with mean quality score <20 were filtered. RNAseq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt
ATAC-seq mapped using bowtie 1.2.2 retaining uniquely mapped pairs only, allowing 2 mismatches. RNAseq mapped to reference using STAR 2.5.2b, in a strand-specific manner
ATAC-seq bedGraphs were generated by filtering duplicates and fragments of length >20 and <150, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts. RNAseq strand-specific coverage tracks were normalized with custom scripts using factors determined by DESeq2 v1.18.1 based on DESeq2 normalization factors and combined with unionBedGraphs and custom scripts (mean count).
Genome_build: dm3
Supplementary_files_format_and_content: ATAC-seq: bedGraph containing combined count of fragment centers for all replicates. RNAseq: bigWig containing combined mean normalized coverage of all replicates for a given treatment.

organism: Drosophila melanogaster

source_name: Drosophila DL1 cells

growth_protocol:
FLAG-tagged IntS11E203Q mutant Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.
Drosophila S2 cells from the DGRC were grown in Shields and Sang M3 (Sigma) media supplemented with bactopeptone (BD Biosciences), yeast extract (Sigma) and 10% FBS (Thermo Fisher Scientific). Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.

extract_protocol:
total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer's instructions.
NA
ATAC-seq experiments: genomic DNA was column extracted following manufacturer's instructions for Qiagen MinElute PCR purification kit. RNA-seq experiments: total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer's instructions.
RNA-seq experiments: Click-Seq Total RNA (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB) from Drosophila DL1 cells treated with Bgal or IntS11 RNAi

treatment_protocol:
IntS11 RNAi
RNA-seq: 3 biological replicates were generated for Control (B-galactosidade treated) in Flag-tagged eGFP control line transgenes or IntS11-depletion (treated with double stranded RNA for IntS11) in Flag-tagged IntS11WT, E203Q mutant, and the eGFP control DL1 cell line transgenes. RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. ATAC-seq: 3 biological replicates using untreated S2 cells were generated.

value: DL1 cells

value: IntS11 RNAi

tag: gender


title: KLF6_v2

description:
Re-analysis of:
GSM2534397 GSM2534396
Raw file(s):
ENCFF762ILJ ENCFF633ZLO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR757EKM


title: KLF9

description:
Re-analysis of:
GSM2534651 GSM2534652
Raw file(s):
ENCFF351KCG ENCFF795MVM
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR938ETG


title: In vitro iMG 60dpi rep 1

value: Biological replicate 1


title: WT1_GpC_100U_45min_MgCl2

value: BY4741 - Replicate 1

value: 3 mM MgCl2


title: KLF16

description:
Re-analysis of:
GSM2527382 GSM2527383
Raw file(s):
ENCFF264ZXH ENCFF380TFO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR009KLQ


title: WT1_CpG_200U_150min_refill_at_90min_MgCl2


title: Wagner_Dmel_DL1_IntS11dep+WTrescue_RNA-seq

growth_protocol:
FLAG-tagged IntS11WT Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.
Drosophila S2 cells from the DGRC were grown in Shields and Sang M3 (Sigma) media supplemented with bactopeptone (BD Biosciences), yeast extract (Sigma) and 10% FBS (Thermo Fisher Scientific). Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.


title: In vitro iMG 10dpi rep 6

source_name: In vitro differentiated microglia 10d

value: Derived from iPS line 657-GFP

value: In vitro differentiated microglia

value: Biological replicate 6


title: WT1_xl_MNase

data_processing:
fastq files were aligned to the SacCer3 genome using Bowtie (Lengmead et al. 2009). Multiple matches were omited.
BAM files were imported into R Studio (RStudio Team, 2015) using GenomicAlignments (Lawrence et al. 2013). Then, reads were shifted by 73 bp to cover the nucleosome dyad and extended to 50 bp. Genome coverage was caluculated.
bedgraph files were generated from genome coverage files using rtracklayer (Lawrence et al. 2009).
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph

extract_protocol:
0.1 g nuclei were washed once and resupended in 200 µl MNase-Buffer. Increasing amounts of MNase (8 U, 16 U, 32 U, 64 U, Sigma) were added per 0.1 g nuclei to obtain varous digestion degrees. Reactions were incubated at 30°C for 20 minutes, stopped by 15 mM EDTA and 0.5% SDS (final conc.), reversed crosslinked if required and DNA was deproteinized by Proteinase K, phenol-chloroform extracted and RNase A digested.
Purified DNA was sheared to ~150 bp fragments with the Covaris S220 and concentrated using the NucleoSpin Gel and PCR Clean-up Kit (Macherey&Nagel). 0.5 – 1 µg as determined by Qubit (ThermoFisher Scientific) was used for library preparation. First, DNA was end polished (15 U T4 DNA Polymerase, 50 U T4 PNK, 5 U Klenow (NEB)) for 30 minutes at 20°C, purified with AmPure XP beads (Beckman Coulter), then subjected to A-tailing (15 U Klenow exo-(NEB)) for 30 minutes at 37°C and purified again. For adapter ligation 15 U T4 DNA Ligase (NEB) and 75 to 150 pmol NEBNext Adaptor or NEBNext Methylated Adaptor for bisulfite conversion were added. The reaction was incubated for 20 minutes at 25°C followed again by AmPure XP bead purification. Half of the end-polished and adapter ligated sample was subjected to 8 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion Polymerase (NEB). Methylated samples were bisulfite converted following the manufacturer’s instructions of the Qiagen EpiTect Bisulfite Kit. 3 µl of the converted sample was subjected to 12-14 cycles of PCR using the NEBNext Multiplex Primers for Illumina and Phusion U Polymerase (ThermoFisher Scientific). All samples were sequenced by LaFuGa (Illumina HiSeq 1500, 50 bp paired-end mode).

tag: crosslinked

value: 20 min


title: Wagner_Dmel_DL1_IntS11dep_RNA-seq

growth_protocol:
FLAG-tagged eGFP Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.
Drosophila S2 cells from the DGRC were grown in Shields and Sang M3 (Sigma) media supplemented with bactopeptone (BD Biosciences), yeast extract (Sigma) and 10% FBS (Thermo Fisher Scientific). Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.


title: In vitro iMG 10dpi rep 5

value: Biological replicate 5


title: Wagner_Dmel_DL1_Control_RNA-seq

treatment_protocol:
Bgal RNAi
RNA-seq: 3 biological replicates were generated for Control (B-galactosidade treated) in Flag-tagged eGFP control line transgenes or IntS11-depletion (treated with double stranded RNA for IntS11) in Flag-tagged IntS11WT, E203Q mutant, and the eGFP control DL1 cell line transgenes. RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. ATAC-seq: 3 biological replicates using untreated S2 cells were generated.

value: Bgal RNAi


title: WT1_CpG_100U_45min_MgCl2

value: CpG

value: BS-seq


title: KDM6A

description:
Raw file(s):
ENCFF297BQB_in_progress ENCFF124DEL_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR288CAD https://www.encodeproject.org/experiments/ENCSR288CAD


title: In vitro iMG 10dpi rep 2


title: In vitro iMG 10dpi rep 4

value: Biological replicate 4


title: KLF10


title: In vitro iMG 10dpi rep 3

value: Biological replicate 3


title: Wagner_Dmel_DL1_IntS1_ChIP-seq

description: Immunoprecipitated DNA with IntS1 antibody

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
ChIPseq read pairs containing one or more members with mean quality score <20 were filtered
ChIP-seq mapped using bowtie 1.2.2 retaining uniquely mapped pairs only, allowing 2 mismatches
ChIP-seq bedGraphs were generated by filtering fragments of length <75 and >500, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3
Supplementary_files_format_and_content: ChIP-seq: bedGraph containing combined count of fragment centers for all replicates

growth_protocol: Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.

extract_protocol:
ChIP-seq experiments: Sonicated genomic DNA was extracted after IP with respective antibody, Phenol-Chloform extracted and ethanol precipitated.
ChIP-seq experiments: NEBNext Ultra II DNA library kit (NEB) on IPed genomic DNA following manufacturer's instructions.

treatment_protocol: ChIP-seq experiments: ChIP-seq libraries were prepared as described in (Henriques et al. 2018) using the NEBNext Ultra II DNA library kit (NEB) following manufacturer's instructions.

value: untreated


title: KAT8

description:
Re-analysis of:
GSM2534669 GSM2534668
Raw file(s):
ENCFF695OMH ENCFF679POI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR954KIC


title: Wagner_Dmel_DL1_IntS12_ChIP-seq

description: Immunoprecipitated DNA with IntS12 antibody


title: KLF11

description:
Re-analysis of:
GSM2534216 GSM2534217
Raw file(s):
ENCFF937ICR ENCFF425ZYO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR616OSG


title: Wagner_Dmel_DL1_Input_ChIP-seq


title: HOMEZ

description:
Re-analysis of:
GSM2527487 GSM2527486
Raw file(s):
ENCFF064SPT ENCFF403YQE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR117CHD

value: FLAG-HOMEZ


title: Wagner_Dmel_DL1_RNA-seq_IntS9dep_rep3

description:
Click-Seq Total RNA (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB) from Drosophila DL1 cells treated with IntS9 dsRNA for 60h
Wagner_dm3_DL1_IntS9dep_N3_depthnorm_coverage_plus.bw
Wagner_dm3_DL1_IntS9dep_N3_depthnorm_coverage_minus.bw

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
RNAseq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt; PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered
RNAseq mapped to reference using STAR 2.5.2b, in a strand-specific manner; PRO-seq mapped to index composed of spike-in genome (mm10), successfully aligned pairs filtered, remaining mapped to reference (dm3) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 1.1.1 retaining uniquely mapped pairs only, allowing 2 mismatches
RNAseq strand-specific coverage tracks were normalized with custom scripts using factors determined by DESeq2 v1.18.1 based on DESeq2 normalization factors and combined with unionBedGraphs and custom scripts (mean count); PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined; ChIP-seq bedGraphs were generated by filtering fragments of length <75 and >350, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3 (RNA-seq, ChIP-seq, PRO-seq), mm10 (PRO-seq)
Supplementary_files_format_and_content: RNAseq: bigWig containing combined mean normalized coverage of all replicates for a given treatment; PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates

growth_protocol: Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061).

extract_protocol: total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer's instructions.

value: DL1 cells

value: IntS9 RNAi treatment


title: HNF1A

description:
Re-analysis of:
GSM2534454 GSM2534453
Raw file(s):
ENCFF442RQA ENCFF194UYN
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR800QIT


title: In vivo iMG 60dpi rep 6

description: 657 iPSCs were reprogrammed from fibroblasts (Couriel) and targetted to express GFP constitutively.

source_name: GFP+ cells from chimeric mouse brain 60 dpi

value: From NSG-Tg(Hu-SCF, GM-CSF, IL-3, CSF1) chimeric mouse


title: Wagner_Dmel_DL1_RNA-seq_IntS9dep_rep2

treatment_protocol: Drosophila DL1 cells treated with IntS9 dsRNA for 60h


title: In vivo iMG 60dpi rep 5


title: In vivo iMG 60dpi rep 4


title: HMGXB4

description:
Raw file(s):
ENCFF088WCY_in_progress ENCFF259JTB_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR174GOO https://www.encodeproject.org/experiments/ENCSR174GOO


title: Wagner_Dmel_DL1_RNA-seq_Bgal_rep3

description:
Click-Seq Total RNA (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB) from Drosophila DL1 cells treated with Bgal dsRNA for 60h
Wagner_dm3_DL1_Control_N3_depthnorm_coverage_plus.bw
Wagner_dm3_DL1_Control_N3_depthnorm_coverage_minus.bw

value: Bgal RNAi treatment


title: HMG20B_v2

description:
Re-analysis of:
GSM2534643 GSM2534642
Raw file(s):
ENCFF510RGT ENCFF713JRT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR925QAW


title: In vivo iMG 60dpi rep 2

value: Biological replicate 2


title: Adelman_Dmel_S2_ATAC-seq

source_name: Drosophila S2 cells

growth_protocol:
Drosophila S2 cells from the DGRC were grown in Shields and Sang M3 (Sigma) media supplemented with bactopeptone (BD Biosciences), yeast extract (Sigma) and 10% FBS (Thermo Fisher Scientific). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.
Drosophila S2 cells from the DGRC were grown in Shields and Sang M3 (Sigma) media supplemented with bactopeptone (BD Biosciences), yeast extract (Sigma) and 10% FBS (Thermo Fisher Scientific). Drosophila DL1 cells were cultured at 25°C in Schneider’s Drosophila medium (Thermo Fisher Scientific 21720024), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30910.03), 1% (v/v) penicillin-streptomycin (Thermo Fisher Scientific 15140122), and 1% (v/v) L-glutamine (Thermo Fisher Scientific 35050061). For all experiments, cells were harvested at a consistent cell density of 4-6x106 cells/ml.

extract_protocol:
Genomic DNA was column extracted following manufacturer's instructions for Qiagen MinElute PCR purification kit. RNA-seq experiments: total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer's instructions.
Nextera DNA Flex Library Prep kit
ATAC-seq experiments: genomic DNA was column extracted following manufacturer's instructions for Qiagen MinElute PCR purification kit. RNA-seq experiments: total RNA was extracted with RNeasy Mini kit (Qiagen) following manufacturer's instructions.
RNA-seq experiments: Click-Seq Total RNA (Jaworski et al. MiMB 2018), with Oligo-d(T) bead selection (NEB) from Drosophila DL1 cells treated with Bgal or IntS11 RNAi

treatment_protocol:
untreated
RNA-seq: 3 biological replicates were generated for Control (B-galactosidade treated) in Flag-tagged eGFP control line transgenes or IntS11-depletion (treated with double stranded RNA for IntS11) in Flag-tagged IntS11WT, E203Q mutant, and the eGFP control DL1 cell line transgenes. RNAi treatments were carried for 60h along with a final concentration of 100 μM CuSO4 to induce transgene expression. ATAC-seq: 3 biological replicates using untreated S2 cells were generated.

value: S2 cells


title: HLF

description:
Re-analysis of:
GSM2534123 GSM2534124
Raw file(s):
ENCFF768KAE ENCFF348HJC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR528PSI

value: FLAG-HLF


title: Wagner_Dmel_DL1_RNA-seq_IntS9dep_rep1


title: In vivo iMG 60dpi rep 3

value: Derived from iPS line 657-GFP


title: HMG20A

description:
Re-analysis of:
GSM2527433 GSM2527434
Raw file(s):
ENCFF402KIC ENCFF261LRY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR072GJV


title: Wagner_Dmel_DL1_RNA-seq_Bgal_rep1

treatment_protocol: Drosophila DL1 cells treated with Bgal dsRNA for 60h


title: HBP1

description:
Re-analysis of:
GSM2534218 GSM2534219
Raw file(s):
ENCFF260FBF ENCFF697NYE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR616WEG


title: Wagner_Dmel_DL1_RNA-seq_Bgal_rep2


title: In vitro iMG 10dpi rep 1

value: In vitro differentiated microglia

value: Biological replicate 1


title: Met-Input

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

data_processing:
Raw data was checked by FastqQC program and trimmed with the Trimmomatic 0.38.
The sequence library was mapped to the reference genome UCSC hg19 using the Bowtie1 program.
Peaks were identified using the MACS2 algorithm.
Regions with p-value < 0.001 (-log10 p-value greater than 3) were considered statistically significant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BED files include peaks.

source_name: H1299 cells

growth_protocol: The lung cancer cell line H1299 (ATCC, CRL-5803) was obtained from the American Type Culture Collection (ATCC). The cells were cultured in RPMI 1640 medium (Lonza, Allendale, NJ) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol: Chromatin immunoprecipitation (ChIP) was performed with the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (#9003, Cell Signaling Technology, Danvers, MA) according to the manufacturer's instructions. Briefly, cells were cross‐linked with 1% formaldehyde (Sigma‐Aldrich) and lysed. Chromatin was digested with micrococcal nuclease into 150-900bp DNA/protein fragments. The fragments were immunoprecipitated with antibodies against H3K4me3 (C42D8, Cell Signaling Technology), H3K27me3 (C36B11, Cell Signaling Technology), or normal rabbit IgG with protein G magnetic beads. Cross-links were reversed, and purified DNAs were then subjected to next-generation sequencing (NovaSeq 6000 System).

treatment_protocol: The cells were treated with or without 5mM metformin (D150959, Sigma-Aldrich, St. Louis, MO).

value: Non-small cell lung cancer cell line

tag: passages

value: Metformin


title: Adelman_Dmel_DL1_PRO-seq_IntS9dep

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
small RNA-seq (hidrolysis fractionation)
IntS9depA_PROseq

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
RNAseq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt; PRO-seq read pairs containing one or more members with mean quality score <20 filtered and trimmed to 50nt, for adapter using cutadapt 1.14, pairs containing reads trimmed shorter than 20 nt filtered
RNAseq mapped to reference using STAR 2.5.2b, in a strand-specific manner; PRO-seq mapped to index composed of spike-in genome (mm10), successfully aligned pairs filtered, remaining mapped to reference (dm3) using bowtie 1.2.2 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 1.1.1 retaining uniquely mapped pairs only, allowing 2 mismatches
RNAseq strand-specific coverage tracks were normalized with custom scripts using factors determined by DESeq2 v1.18.1 based on DESeq2 normalization factors and combined with unionBedGraphs and custom scripts (mean count); PROseq strand-specific bedGraphs generated using custom scripts based on 3' mapping location of end 1 reads only, with all replicates combined; ChIP-seq bedGraphs were generated by filtering fragments of length <75 and >350, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3 (RNA-seq, ChIP-seq, PRO-seq)
Supplementary_files_format_and_content: RNAseq: bigWig containing combined mean normalized coverage of all replicates for a given treatment; PRO-seq: bedGraph containing combined count of end 1 3' mapping locations for all replicates for a given treatment; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates

extract_protocol:
nascent biotin-labeled RNA was isolated from permeabilized cells using Total RNA Purification kit (Norgen Biotek Corp.)
Custom library preparation

treatment_protocol: Drosophila DL1 cells treated with IntS9 dsRNA for 3 days without CuSO4 induction

tag: molecule subtype

value: biotin labeled nascent RNA


title: In vivo iMG 10dpi rep 6

source_name: GFP+ cells from chimeric mouse brain 10 dpi

tag: cell type

value: Biological replicate 6


title: In vivo iMG 60dpi rep 1


title: In vivo iMG 10dpi rep 5

value: Biological replicate 5


title: GMEB2

description:
Re-analysis of:
GSM2534382 GSM2534381
Raw file(s):
ENCFF158NYT ENCFF096ZDV
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR745VSQ

data_processing:
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates and 2 controls
ChIP-seq fastqs and ChIP-seq controls were aligned to hg19 genome assembly using BWA-0.7.12(Burrows Wheeler Aligner)
Post-alignment filtering was performed using samtools with MAPQ_THRESH=30 & picard-tools-1.88 to remove the duplicates
Peak enrichment was computed using phantompeakqualtools, implementing SPP peak calling algorithm, to generate narrowpeaks
IDR was run on replicates peak file and pooled peaks, using idr-2.0.2 tool, to generate peaks passing IDR cutoff 0.02 (soft-idr-threshold) followed by filtering of ENCODE blacklisted regions
Genome_build: hg19 male
Supplementary_files_format_and_content: NarrowPeak files are in BED6+4 format with 10 tab-delimited columns [chrom ,chromStart ,chromEnd ,name ,score ,strand ,signalValue ,pValue(-log10) ,qValue(-log10) , peak]; -1 used if no pValue, qValue assigned.

extract_protocol:
Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol.
Illumina Single End for ChIP-seq


title: Adelman_Dmel_DL1_PRO-seq_Bgal

description:
biotin labeled nascent RNA isolated from Drosophila DL1 permeabilized cells
small RNA-seq (hidrolysis fractionation)
BgalA_PROseq

treatment_protocol: Drosophila DL1 cells treated with Bgal dsRNA for 3 days without CuSO4 induction


title: Met-H3K27me3

value: H3K27me3 (C36B11, Cell Signaling Technology)


title: In vivo iMG 10dpi rep 4

value: Biological replicate 4


title: Con-H3K27me3


title: E18 cerebral cortex

city: Shanghai

first: Peng

last: Jian

address: 320 Yue Yang Road

department: Institute of Neuroscience

country: China

institute: University of Chinese Academy of Sciences

data_processing:
Basecalls performed using Cellranger 2.1
reads were aligned to the mm10 genome assembly using cellranger 2.1 with the following configurations…
cellranger count --id=result --transcriptome=/ion/luozg_group/pengjian/2_refdata/1_mm/refdata-cellranger-mm10-1.2.0 --fastqs=/ion/luozg_group/pengjian/1_rawdata --sample=CR --expect-cells=5000
Data were filtered using the following specifications…filtering out outliers with extremely low (less than 200) and high (more than 6500) gene numbers
Cluster were perform using Seurat in R
26 bp Read1 (10× cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert)is biological,otherwise is technical
Genome_build: mm10
Supplementary_files_format_and_content: raw counts; column head (E18_cerebral cortex.csv) is barcode sequence (16bp) for each cell ID, each row represents the genes that had detected

source_name: superficial cerebral cortex cell

extract_protocol:
Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and digested for 15 min in 0.25% trypsin solution
All procedures followed the guidelines provided by 10x Genomics, Inc Dissociated cells in each sample were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) in a limiting dilution to lower multiplet rate. Then, single-cell GEMs were incubated with reverse-transcription reagents, including several primers for cell and transcript barcoding in cDNA synthesis, followed by cDNA amplification and library construction

tag: developmental stage

tag: tissue

value: cerebral cortex


title: GATAD1

description:
Re-analysis of:
GSM2527474 GSM2527475
Raw file(s):
ENCFF495VRD ENCFF461VNE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR108TYQ


title: Met-H3K4me3

value: H3K4me3 (C42D8, Cell Signaling Technology)


title: GATA4

description:
Re-analysis of:
GSM2534193 GSM2534192
Raw file(s):
ENCFF163SRP ENCFF193ROJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR590CNM


title: Con-Input


title: In vivo iMG 10dpi rep 2

value: From NSG-Tg(Hu-SCF, GM-CSF, IL-3, CSF1) chimeric mouse


title: GABPA

description:
Re-analysis of:
GSM2527661 GSM2527662
Raw file(s):
ENCFF350SEQ ENCFF921JLH
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR269TNX

value: FLAG-GABPA


title: In vivo iMG 10dpi rep 3

value: Biological replicate 3


title: Con-H3K4me3


title: GATAD2A

description:
Re-analysis of:
GSM2534641 GSM2534640
Raw file(s):
ENCFF113FFZ ENCFF685OLC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR925BFV


title: In vivo iMG 10dpi rep 1


title: Metformin [RNA-seq]

data_processing:
After sequencing, the low-quality reads and PCR duplicates were removed by Trimmomatic 0.38.
The trimmed sequences were then assembled into reference transcripts using the HISAT2 program.
The read count was normalized into a value of FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and the reads with a value of zero were excluded.
Significantly up- or down-regulated genes were identified by cutoff value of |FC| >= 1.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene_abund.anno.tab: Tab-delimited text files include FPKM and TPM values.

extract_protocol:
Total RNA was isolated from cultured H1299 cells using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). DNA contamination was removed using DNase, and the remaining RNA was broken into short fragments. The RNA fragments were reverse transcribed into cDNA, ligated with adaptors, and PCR amplified. The amplified cDNAs were then selected by a range of sizes and sequenced using a next-generation sequencing device (NovaSeq 6000 System).
The sequence library was mapped to the reference genome UCSC hg19 using the Bowtie2 program.


title: iMP6

source_name: Microglial precursors

value: Common Precursor cell


title: FOXA2

source_name: HepG2 cells


title: ETV4

description:
Re-analysis of:
GSM2534353 GSM2534352
Raw file(s):
ENCFF658DDY ENCFF162GLI
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR714YZG


title: iMP5


title: FOXA3

description:
Re-analysis of:
GSM2527454 GSM2527455
Raw file(s):
ENCFF807WOU ENCFF492CBJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR092OVN


title: iMP2

value: Biological replicate 2


title: EZH2

description:
Re-analysis of:
GSM1003487
Raw file(s):
ENCFF000BEL ENCFF000BEQ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR000ARI


title: GABPB1_v2

description:
Re-analysis of:
GSM2534043 GSM2534044
Raw file(s):
ENCFF079HKK ENCFF104LBO
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR462KYU


title: iMP3

description: 657 iPSCs were reprogrammed from fibroblasts (Couriel) and targetted to express GFP constitutively.

value: Derived from iPS line 657-GFP


title: JQ1-2

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 “TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35”
MAPPING - STAR_2.6.0c “--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical”
READ COUNTING - subread-1.6.1 “featurecounts, -s 2 -t exon -g gene_name”
Genome_build: GRCh38.p12 (hg38) + Gencode-28 Annotation
Supplementary_files_format_and_content: normalized abundance

growth_protocol: Human umbilical vein endothelial cells (HUVECs, Cell Application Inc.) were cultured in M200 media supplemented with 5% FBS, 1X ECGS ( Cell Application Inc.) and 1X antibiotics.

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Confluent HUVECs were treated with BRD4 inhibitor (+)-JQ1 (10 uM, in 0.1% DMSO) for 48 h before RNA was collected for genome-wide RNA-sequencing, n=2 different donors.

value: Human umbilical vein endothelial cells (HUVECs)

value: 10 uM BRD4 inhibitor (+)-JQ1 for 48hrs


title: iMP4


title: iMP1

value: Biological replicate 1


title: DRAP1

description:
Re-analysis of:
GSM2534416 GSM2534417
Raw file(s):
ENCFF024PSP ENCFF128NBF
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR765MKZ


title: ELF3

description:
Re-analysis of:
GSM2534422 GSM2534421
Raw file(s):
ENCFF873VOO ENCFF856RPX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR770AOR


title: JQ1-1


title: DNMT3B

description:
Re-analysis of:
GSM2527538 GSM2527537
Raw file(s):
ENCFF699XDW ENCFF470IAE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR156CWW


title: veh2

value: vehicle control


title: WT4_xl_CpG_2U_240min_refill_at_180min_NP-seq

data_processing:
basecalling with Albacore v2.3.3
Library strategy: ODM-seq
ODM-seq analysis for Nanopore-seq data  We called the bases with Albacore (Oxford Nanopore Technologies, version 2.3.3) or Guppy (Oxford Nanopore Technologies, version 3.2.2), for WT4 and WT5, respectively, and mapped the reads with minimap2 (version 2.14-r892-dirty, (Li 2018)). For methylation calling we used Nanopolish (version 0.11.0, (Simpson et al. 2017)). At each CpG methylation site, the occupancy is calculated as ratio of unmethylated reads over the sum of methylated and unmethylated reads, ignoring reads where the site has been called "ambiguous" by Nanopolish. We ignored methylation sites with a coverage less than 20. Note that, currently, Nanopolish groups CpG sites within 10 bp into one site, thus having a lower resolution than BS-seq.
tsv files contain columns with the absolute occupancy value, the strand, the motif and the number of converted as well as the total number of reads for each methyation site.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph. Tsv

extract_protocol:
Nuclei pellets were washed in methylation buffer (20 mM HEPES-NaOH pH 7.5, 70 mM NaCl, 0.25 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.5% (v/v) glycerol, 1 mM DTT, 0.25 mM PMSF (Darst et al. 2012)). Per reaction, nuclei from ca. 0.1 g wet cell pellet were resuspended in 800 µl methylation buffer containing 640 µM freshly added S-adenosylmethionine (SAM). 200 U M.SssI or M.CviPI (both NEB) and 10 mM DTT were freshly added. Methylation reactions were dialyzed in Slide-A-Lyzer MINI Dialysis Devices 10 K MWCO (Thermo Fisher Scientific) against 15 ml methylation buffer with 200 µM freshly added SAM at 25°C for M.SssI or 37°C for M.CviPI. 0.5 - 1 µg fully assembled pUC19-601-25mer plasmid (pFMP233) (Lowary and Widom 1998; Lieleg et al. 2015a) and SGD assembled Escherichia coli gDNA or SGD assembled E. coli plasmid library (limited Sau3A fragments of E. coli gDNA ligated into pJET 1.2 plasmid (Thermo Fisher Scientific)) was spiked-in prior to methylase addition. E. coli spike-in results were not further pursued due to low coverage. Reactions were stopped by 0.5% SDS (final conc.), reversed crosslinked if required and DNA was deproteinized by Proteinase K, phenol-chloroform extracted and RNase A digested.
Oxford Nanopore library construction and sequencing  For Nanopore sequencing, 1 µg of purified DNA was subjected to 1D native barcoding (Oxford Nanopore, SQK-LSK109). To get up to 1 Gbases coverage per sample, up to five samples were loaded to a MinION flowcell (R9.4.1).

tag: methyltransferase

value: CpG

value: 20 min


title: DMAP1

description:
Re-analysis of:
GSM2534292 GSM2534293
Raw file(s):
ENCFF118UPE ENCFF039MUL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR670YPQ